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revision 1.27 by cnh, Thu Oct 14 14:24:28 2004 UTC revision 1.37 by molod, Wed Jun 28 16:48:19 2006 UTC
# Line 17  you are ready to try implementing the co Line 17  you are ready to try implementing the co
17    
18  \section{Where to find information}  \section{Where to find information}
19  \label{sect:whereToFindInfo}  \label{sect:whereToFindInfo}
20    \begin{rawhtml}
21    <!-- CMIREDIR:whereToFindInfo: -->
22    \end{rawhtml}
23    
24  A web site is maintained for release 2 (``Pelican'') of MITgcm:  There is a web-archived support mailing list for the model that
 \begin{rawhtml} <A href=http://mitgcm.org/pelican/ target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/pelican  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 Here you will find an on-line version of this document, a  
 ``browsable'' copy of the code and a searchable database of the model  
 and site, as well as links for downloading the model and  
 documentation, to data-sources, and other related sites.  
   
 There is also a web-archived support mailing list for the model that  
25  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:  you can email at \texttt{MITgcm-support@mitgcm.org} or browse at:
26  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href=http://mitgcm.org/mailman/listinfo/mitgcm-support/ target="idontexist"> \end{rawhtml}
27  \begin{verbatim}  \begin{verbatim}
# Line 37  http://mitgcm.org/mailman/listinfo/mitgc Line 29  http://mitgcm.org/mailman/listinfo/mitgc
29  http://mitgcm.org/pipermail/mitgcm-support/  http://mitgcm.org/pipermail/mitgcm-support/
30  \end{verbatim}  \end{verbatim}
31  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
 Essentially all of the MITgcm web pages can be searched using a  
 popular web crawler such as Google or through our own search facility:  
 \begin{rawhtml} <A href=http://mitgcm.org/mailman/htdig/ target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/htdig/  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 %%% http://www.google.com/search?q=hydrostatic+site%3Amitgcm.org  
   
   
32    
33  \section{Obtaining the code}  \section{Obtaining the code}
34  \label{sect:obtainingCode}  \label{sect:obtainingCode}
35    \begin{rawhtml}
36    <!-- CMIREDIR:obtainingCode: -->
37    \end{rawhtml}
38    
39  MITgcm can be downloaded from our system by following  MITgcm can be downloaded from our system by following
40  the instructions below. As a courtesy we ask that you send e-mail to us at  the instructions below. As a courtesy we ask that you send e-mail to us at
# Line 92  be set within your shell.  For a csh or Line 77  be set within your shell.  For a csh or
77  \begin{verbatim}  \begin{verbatim}
78  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack  % setenv CVSROOT :pserver:cvsanon@mitgcm.org:/u/gcmpack
79  \end{verbatim}  \end{verbatim}
80  in your .cshrc or .tcshrc file.  For bash or sh shells, put:  in your \texttt{.cshrc} or \texttt{.tcshrc} file.  For bash or sh
81    shells, put:
82  \begin{verbatim}  \begin{verbatim}
83  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'  % export CVSROOT=':pserver:cvsanon@mitgcm.org:/u/gcmpack'
84  \end{verbatim}  \end{verbatim}
# Line 118  The MITgcm web site contains further dir Line 104  The MITgcm web site contains further dir
104  code and CVS.  It also contains a web interface to our CVS archive so  code and CVS.  It also contains a web interface to our CVS archive so
105  that one may easily view the state of files, revisions, and other  that one may easily view the state of files, revisions, and other
106  development milestones:  development milestones:
107  \begin{rawhtml} <A href=''http://mitgcm.org/download'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/download" target="idontexist"> \end{rawhtml}
108  \begin{verbatim}  \begin{verbatim}
109  http://mitgcm.org/source_code.html  http://mitgcm.org/source_code.html
110  \end{verbatim}  \end{verbatim}
# Line 147  of CVS aliases Line 133  of CVS aliases
133    \label{tab:cvsModules}    \label{tab:cvsModules}
134  \end{table}  \end{table}
135    
136  The checkout process creates a directory called \textit{MITgcm}. If  The checkout process creates a directory called \texttt{MITgcm}. If
137  the directory \textit{MITgcm} exists this command updates your code  the directory \texttt{MITgcm} exists this command updates your code
138  based on the repository. Each directory in the source tree contains a  based on the repository. Each directory in the source tree contains a
139  directory \textit{CVS}. This information is required by CVS to keep  directory \texttt{CVS}. This information is required by CVS to keep
140  track of your file versions with respect to the repository. Don't edit  track of your file versions with respect to the repository. Don't edit
141  the files in \textit{CVS}!  You can also use CVS to download code  the files in \texttt{CVS}!  You can also use CVS to download code
142  updates.  More extensive information on using CVS for maintaining  updates.  More extensive information on using CVS for maintaining
143  MITgcm code can be found  MITgcm code can be found
144  \begin{rawhtml} <A href=''http://mitgcm.org/usingcvstoget.html'' target="idontexist"> \end{rawhtml}  \begin{rawhtml} <A href="http://mitgcm.org/usingcvstoget.html" target="idontexist"> \end{rawhtml}
145  here  here
146  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
147  .  .
# Line 168  they create can be changed to a differen Line 154  they create can be changed to a differen
154     %  mv MITgcm MITgcm_verif_basic     %  mv MITgcm MITgcm_verif_basic
155  \end{verbatim}  \end{verbatim}
156    
   
 \subsection{Method 2 - Tar file download}  
 \label{sect:conventionalDownload}  
   
 If you do not have CVS on your system, you can download the model as a  
 tar file from the web site at:  
 \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}  
 \begin{verbatim}  
 http://mitgcm.org/download/  
 \end{verbatim}  
 \begin{rawhtml} </A> \end{rawhtml}  
 The tar file still contains CVS information which we urge you not to  
 delete; even if you do not use CVS yourself the information can help  
 us if you should need to send us your copy of the code.  If a recent  
 tar file does not exist, then please contact the developers through  
 the  
 \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  
 MITgcm-support@mitgcm.org  
 \begin{rawhtml} </A> \end{rawhtml}  
 mailing list.  
   
157  \subsubsection{Upgrading from an earlier version}  \subsubsection{Upgrading from an earlier version}
158    
159  If you already have an earlier version of the code you can ``upgrade''  If you already have an earlier version of the code you can ``upgrade''
# Line 255  that you may only have part of a patch. Line 220  that you may only have part of a patch.
220  also means we can't tell what version of the code you are working  also means we can't tell what version of the code you are working
221  with. So please be sure you understand what you're doing.  with. So please be sure you understand what you're doing.
222    
223    \subsection{Method 2 - Tar file download}
224    \label{sect:conventionalDownload}
225    
226    If you do not have CVS on your system, you can download the model as a
227    tar file from the web site at:
228    \begin{rawhtml} <A href=http://mitgcm.org/download target="idontexist"> \end{rawhtml}
229    \begin{verbatim}
230    http://mitgcm.org/download/
231    \end{verbatim}
232    \begin{rawhtml} </A> \end{rawhtml}
233    The tar file still contains CVS information which we urge you not to
234    delete; even if you do not use CVS yourself the information can help
235    us if you should need to send us your copy of the code.  If a recent
236    tar file does not exist, then please contact the developers through
237    the
238    \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
239    MITgcm-support@mitgcm.org
240    \begin{rawhtml} </A> \end{rawhtml}
241    mailing list.
242    
243  \section{Model and directory structure}  \section{Model and directory structure}
244    \begin{rawhtml}
245    <!-- CMIREDIR:directory_structure: -->
246    \end{rawhtml}
247    
248  The ``numerical'' model is contained within a execution environment  The ``numerical'' model is contained within a execution environment
249  support wrapper. This wrapper is designed to provide a general  support wrapper. This wrapper is designed to provide a general
# Line 263  framework for grid-point models. MITgcmU Line 251  framework for grid-point models. MITgcmU
251  model that uses the framework. Under this structure the model is split  model that uses the framework. Under this structure the model is split
252  into execution environment support code and conventional numerical  into execution environment support code and conventional numerical
253  model code. The execution environment support code is held under the  model code. The execution environment support code is held under the
254  \textit{eesupp} directory. The grid point model code is held under the  \texttt{eesupp} directory. The grid point model code is held under the
255  \textit{model} directory. Code execution actually starts in the  \texttt{model} directory. Code execution actually starts in the
256  \textit{eesupp} routines and not in the \textit{model} routines. For  \texttt{eesupp} routines and not in the \texttt{model} routines. For
257  this reason the top-level \textit{MAIN.F} is in the  this reason the top-level \texttt{MAIN.F} is in the
258  \textit{eesupp/src} directory. In general, end-users should not need  \texttt{eesupp/src} directory. In general, end-users should not need
259  to worry about this level. The top-level routine for the numerical  to worry about this level. The top-level routine for the numerical
260  part of the code is in \textit{model/src/THE\_MODEL\_MAIN.F}. Here is  part of the code is in \texttt{model/src/THE\_MODEL\_MAIN.F}. Here is
261  a brief description of the directory structure of the model under the  a brief description of the directory structure of the model under the
262  root tree (a detailed description is given in section 3: Code  root tree (a detailed description is given in section 3: Code
263  structure).  structure).
264    
265  \begin{itemize}  \begin{itemize}
266    
267  \item \textit{bin}: this directory is initially empty. It is the  \item \texttt{doc}: contains brief documentation notes.
   default directory in which to compile the code.  
     
 \item \textit{diags}: contains the code relative to time-averaged  
   diagnostics. It is subdivided into two subdirectories \textit{inc}  
   and \textit{src} that contain include files (*.\textit{h} files) and  
   Fortran subroutines (*.\textit{F} files), respectively.  
   
 \item \textit{doc}: contains brief documentation notes.  
268        
269  \item \textit{eesupp}: contains the execution environment source code.  \item \texttt{eesupp}: contains the execution environment source code.
270    Also subdivided into two subdirectories \textit{inc} and    Also subdivided into two subdirectories \texttt{inc} and
271    \textit{src}.    \texttt{src}.
272      
273    \item \texttt{model}: this directory contains the main source code.
274      Also subdivided into two subdirectories \texttt{inc} and
275      \texttt{src}.
276        
277  \item \textit{exe}: this directory is initially empty. It is the  \item \texttt{pkg}: contains the source code for the packages. Each
278    default directory in which to execute the code.    package corresponds to a subdirectory. For example, \texttt{gmredi}
     
 \item \textit{model}: this directory contains the main source code.  
   Also subdivided into two subdirectories \textit{inc} and  
   \textit{src}.  
     
 \item \textit{pkg}: contains the source code for the packages. Each  
   package corresponds to a subdirectory. For example, \textit{gmredi}  
279    contains the code related to the Gent-McWilliams/Redi scheme,    contains the code related to the Gent-McWilliams/Redi scheme,
280    \textit{aim} the code relative to the atmospheric intermediate    \texttt{aim} the code relative to the atmospheric intermediate
281    physics. The packages are described in detail in section 3.    physics. The packages are described in detail in chapter \ref{chap.packagesI}.
282        
283  \item \textit{tools}: this directory contains various useful tools.  \item \texttt{tools}: this directory contains various useful tools.
284    For example, \textit{genmake2} is a script written in csh (C-shell)    For example, \texttt{genmake2} is a script written in csh (C-shell)
285    that should be used to generate your makefile. The directory    that should be used to generate your makefile. The directory
286    \textit{adjoint} contains the makefile specific to the Tangent    \texttt{adjoint} contains the makefile specific to the Tangent
287    linear and Adjoint Compiler (TAMC) that generates the adjoint code.    linear and Adjoint Compiler (TAMC) that generates the adjoint code.
288    The latter is described in details in part V.    The latter is described in detail in part \ref{chap.ecco}.
289      This directory also contains the subdirectory build\_options, which
290      contains the `optfiles' with the compiler options for the different
291      compilers and machines that can run MITgcm.
292        
293  \item \textit{utils}: this directory contains various utilities. The  \item \texttt{utils}: this directory contains various utilities. The
294    subdirectory \textit{knudsen2} contains code and a makefile that    subdirectory \texttt{knudsen2} contains code and a makefile that
295    compute coefficients of the polynomial approximation to the knudsen    compute coefficients of the polynomial approximation to the knudsen
296    formula for an ocean nonlinear equation of state. The    formula for an ocean nonlinear equation of state. The
297    \textit{matlab} subdirectory contains matlab scripts for reading    \texttt{matlab} subdirectory contains matlab scripts for reading
298    model output directly into matlab. \textit{scripts} contains C-shell    model output directly into matlab. \texttt{scripts} contains C-shell
299    post-processing scripts for joining processor-based and tiled-based    post-processing scripts for joining processor-based and tiled-based
300    model output.    model output. The subdirectory exch2 contains the code needed for
301      the exch2 package to work with different combinations of domain
302      decompositions.
303        
304  \item \textit{verification}: this directory contains the model  \item \texttt{verification}: this directory contains the model
305    examples. See section \ref{sect:modelExamples}.    examples. See section \ref{sect:modelExamples}.
306    
307  \end{itemize}  \item \texttt{jobs}: contains sample job scripts for running MITgcm.
   
 \section[MITgcm Example Experiments]{Example experiments}  
 \label{sect:modelExamples}  
   
 %% a set of twenty-four pre-configured numerical experiments  
   
 The MITgcm distribution comes with more than a dozen pre-configured  
 numerical experiments. Some of these example experiments are tests of  
 individual parts of the model code, but many are fully fledged  
 numerical simulations. A few of the examples are used for tutorial  
 documentation in sections \ref{sect:eg-baro} - \ref{sect:eg-global}.  
 The other examples follow the same general structure as the tutorial  
 examples. However, they only include brief instructions in a text file  
 called {\it README}.  The examples are located in subdirectories under  
 the directory \textit{verification}. Each example is briefly described  
 below.  
   
 \subsection{Full list of model examples}  
   
 \begin{enumerate}  
     
 \item \textit{exp0} - single layer, ocean double gyre (barotropic with  
   free-surface). This experiment is described in detail in section  
   \ref{sect:eg-baro}.  
   
 \item \textit{exp1} - Four layer, ocean double gyre. This experiment  
   is described in detail in section \ref{sect:eg-baroc}.  
     
 \item \textit{exp2} - 4x4 degree global ocean simulation with steady  
   climatological forcing. This experiment is described in detail in  
   section \ref{sect:eg-global}.  
     
 \item \textit{exp4} - Flow over a Gaussian bump in open-water or  
   channel with open boundaries.  
     
 \item \textit{exp5} - Inhomogenously forced ocean convection in a  
   doubly periodic box.  
   
 \item \textit{front\_relax} - Relaxation of an ocean thermal front (test for  
 Gent/McWilliams scheme). 2D (Y-Z).  
   
 \item \textit{internal wave} - Ocean internal wave forced by open  
   boundary conditions.  
308        
309  \item \textit{natl\_box} - Eastern subtropical North Atlantic with KPP  \item \texttt{lsopt}: Line search code used for optimization.
   scheme; 1 month integration  
310        
311  \item \textit{hs94.1x64x5} - Zonal averaged atmosphere using Held and  \item \texttt{optim}: Interface between MITgcm and line search code.
   Suarez '94 forcing.  
312        
 \item \textit{hs94.128x64x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing.  
     
 \item \textit{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and  
   Suarez '94 forcing on the cubed sphere.  
     
 \item \textit{aim.5l\_zon-ave} - Intermediate Atmospheric physics.  
   Global Zonal Mean configuration, 1x64x5 resolution.  
     
 \item \textit{aim.5l\_XZ\_Equatorial\_Slice} - Intermediate  
   Atmospheric physics, equatorial Slice configuration.  2D (X-Z).  
     
 \item \textit{aim.5l\_Equatorial\_Channel} - Intermediate Atmospheric  
   physics. 3D Equatorial Channel configuration.  
     
 \item \textit{aim.5l\_LatLon} - Intermediate Atmospheric physics.  
   Global configuration, on latitude longitude grid with 128x64x5 grid  
   points ($2.8^\circ{\rm degree}$ resolution).  
     
 \item \textit{adjustment.128x64x1} Barotropic adjustment problem on  
   latitude longitude grid with 128x64 grid points ($2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{adjustment.cs-32x32x1} Barotropic adjustment problem on  
   cube sphere grid with 32x32 points per face ( roughly $2.8^\circ{\rm  
     degree}$ resolution).  
     
 \item \textit{advect\_cs} Two-dimensional passive advection test on  
   cube sphere grid.  
     
 \item \textit{advect\_xy} Two-dimensional (horizontal plane) passive  
   advection test on Cartesian grid.  
     
 \item \textit{advect\_yz} Two-dimensional (vertical plane) passive  
   advection test on Cartesian grid.  
     
 \item \textit{carbon} Simple passive tracer experiment. Includes  
   derivative calculation. Described in detail in section  
   \ref{sect:eg-carbon-ad}.  
   
 \item \textit{flt\_example} Example of using float package.  
     
 \item \textit{global\_ocean.90x40x15} Global circulation with GM, flux  
   boundary conditions and poles.  
   
 \item \textit{global\_ocean\_pressure} Global circulation in pressure  
   coordinate (non-Boussinesq ocean model). Described in detail in  
   section \ref{sect:eg-globalpressure}.  
     
 \item \textit{solid-body.cs-32x32x1} Solid body rotation test for cube  
   sphere grid.  
   
 \end{enumerate}  
   
 \subsection{Directory structure of model examples}  
   
 Each example directory has the following subdirectories:  
   
 \begin{itemize}  
 \item \textit{code}: contains the code particular to the example. At a  
   minimum, this directory includes the following files:  
   
   \begin{itemize}  
   \item \textit{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to  
     the ``execution environment'' part of the code. The default  
     version is located in \textit{eesupp/inc}.  
     
   \item \textit{code/CPP\_OPTIONS.h}: declares CPP keys relative to  
     the ``numerical model'' part of the code. The default version is  
     located in \textit{model/inc}.  
     
   \item \textit{code/SIZE.h}: declares size of underlying  
     computational grid.  The default version is located in  
     \textit{model/inc}.  
   \end{itemize}  
     
   In addition, other include files and subroutines might be present in  
   \textit{code} depending on the particular experiment. See Section 2  
   for more details.  
     
 \item \textit{input}: contains the input data files required to run  
   the example. At a minimum, the \textit{input} directory contains the  
   following files:  
   
   \begin{itemize}  
   \item \textit{input/data}: this file, written as a namelist,  
     specifies the main parameters for the experiment.  
     
   \item \textit{input/data.pkg}: contains parameters relative to the  
     packages used in the experiment.  
     
   \item \textit{input/eedata}: this file contains ``execution  
     environment'' data. At present, this consists of a specification  
     of the number of threads to use in $X$ and $Y$ under multithreaded  
     execution.  
   \end{itemize}  
     
   In addition, you will also find in this directory the forcing and  
   topography files as well as the files describing the initial state  
   of the experiment.  This varies from experiment to experiment. See  
   section 2 for more details.  
   
 \item \textit{results}: this directory contains the output file  
   \textit{output.txt} produced by the simulation example. This file is  
   useful for comparison with your own output when you run the  
   experiment.  
313  \end{itemize}  \end{itemize}
314    
 Once you have chosen the example you want to run, you are ready to  
 compile the code.  
   
315  \section[Building MITgcm]{Building the code}  \section[Building MITgcm]{Building the code}
316  \label{sect:buildingCode}  \label{sect:buildingCode}
317    \begin{rawhtml}
318  To compile the code, we use the {\em make} program. This uses a file  <!-- CMIREDIR:buildingCode: -->
319  ({\em Makefile}) that allows us to pre-process source files, specify  \end{rawhtml}
320  compiler and optimization options and also figures out any file  
321  dependencies. We supply a script ({\em genmake2}), described in  To compile the code, we use the \texttt{make} program. This uses a
322  section \ref{sect:genmake}, that automatically creates the {\em  file (\texttt{Makefile}) that allows us to pre-process source files,
323    Makefile} for you. You then need to build the dependencies and  specify compiler and optimization options and also figures out any
324    file dependencies. We supply a script (\texttt{genmake2}), described
325    in section \ref{sect:genmake}, that automatically creates the
326    \texttt{Makefile} for you. You then need to build the dependencies and
327  compile the code.  compile the code.
328    
329  As an example, let's assume that you want to build and run experiment  As an example, assume that you want to build and run experiment
330  \textit{verification/exp2}. The are multiple ways and places to  \texttt{verification/exp2}. The are multiple ways and places to
331  actually do this but here let's build the code in  actually do this but here let's build the code in
332  \textit{verification/exp2/input}:  \texttt{verification/exp2/build}:
333  \begin{verbatim}  \begin{verbatim}
334  % cd verification/exp2/input  % cd verification/exp2/build
335  \end{verbatim}  \end{verbatim}
336  First, build the {\em Makefile}:  First, build the \texttt{Makefile}:
337  \begin{verbatim}  \begin{verbatim}
338  % ../../../tools/genmake2 -mods=../code  % ../../../tools/genmake2 -mods=../code
339  \end{verbatim}  \end{verbatim}
340  The command line option tells {\em genmake} to override model source  The command line option tells \texttt{genmake} to override model source
341  code with any files in the directory {\em ./code/}.  code with any files in the directory \texttt{../code/}.
342    
343  On many systems, the {\em genmake2} program will be able to  On many systems, the \texttt{genmake2} program will be able to
344  automatically recognize the hardware, find compilers and other tools  automatically recognize the hardware, find compilers and other tools
345  within the user's path (``echo \$PATH''), and then choose an  within the user's path (``\texttt{echo \$PATH}''), and then choose an
346  appropriate set of options from the files contained in the {\em  appropriate set of options from the files (``optfiles'') contained in
347    tools/build\_options} directory.  Under some circumstances, a user  the \texttt{tools/build\_options} directory.  Under some
348  may have to create a new ``optfile'' in order to specify the exact  circumstances, a user may have to create a new ``optfile'' in order to
349  combination of compiler, compiler flags, libraries, and other options  specify the exact combination of compiler, compiler flags, libraries,
350  necessary to build a particular configuration of MITgcm.  In such  and other options necessary to build a particular configuration of
351  cases, it is generally helpful to read the existing ``optfiles'' and  MITgcm.  In such cases, it is generally helpful to read the existing
352  mimic their syntax.  ``optfiles'' and mimic their syntax.
353    
354  Through the MITgcm-support list, the MITgcm developers are willing to  Through the MITgcm-support list, the MITgcm developers are willing to
355  provide help writing or modifing ``optfiles''.  And we encourage users  provide help writing or modifing ``optfiles''.  And we encourage users
356  to post new ``optfiles'' (particularly ones for new machines or  to post new ``optfiles'' (particularly ones for new machines or
357  architectures) to the  architectures) to the
358  \begin{rawhtml} <A href=''mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}  \begin{rawhtml} <A href="mailto:MITgcm-support@mitgcm.org"> \end{rawhtml}
359  MITgcm-support@mitgcm.org  MITgcm-support@mitgcm.org
360  \begin{rawhtml} </A> \end{rawhtml}  \begin{rawhtml} </A> \end{rawhtml}
361  list.  list.
362    
363  To specify an optfile to {\em genmake2}, the syntax is:  To specify an optfile to \texttt{genmake2}, the syntax is:
364  \begin{verbatim}  \begin{verbatim}
365  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile  % ../../../tools/genmake2 -mods=../code -of /path/to/optfile
366  \end{verbatim}  \end{verbatim}
367    
368  Once a {\em Makefile} has been generated, we create the dependencies:  Once a \texttt{Makefile} has been generated, we create the
369    dependencies with the command:
370  \begin{verbatim}  \begin{verbatim}
371  % make depend  % make depend
372  \end{verbatim}  \end{verbatim}
373  This modifies the {\em Makefile} by attaching a [long] list of files  This modifies the \texttt{Makefile} by attaching a (usually, long)
374  upon which other files depend. The purpose of this is to reduce  list of files upon which other files depend. The purpose of this is to
375  re-compilation if and when you start to modify the code. The {\tt make  reduce re-compilation if and when you start to modify the code. The
376    depend} command also creates links from the model source to this  {\tt make depend} command also creates links from the model source to
377  directory.  this directory.  It is important to note that the {\tt make depend}
378    stage will occasionally produce warnings or errors since the
379    dependency parsing tool is unable to find all of the necessary header
380    files (\textit{eg.}  \texttt{netcdf.inc}).  In these circumstances, it
381    is usually OK to ignore the warnings/errors and proceed to the next
382    step.
383    
384  Next compile the code:  Next one can compile the code using:
385  \begin{verbatim}  \begin{verbatim}
386  % make  % make
387  \end{verbatim}  \end{verbatim}
388  The {\tt make} command creates an executable called \textit{mitgcmuv}.  The {\tt make} command creates an executable called \texttt{mitgcmuv}.
389  Additional make ``targets'' are defined within the makefile to aid in  Additional make ``targets'' are defined within the makefile to aid in
390  the production of adjoint and other versions of MITgcm.  the production of adjoint and other versions of MITgcm.  On SMP
391    (shared multi-processor) systems, the build process can often be sped
392    up appreciably using the command:
393    \begin{verbatim}
394    % make -j 2
395    \end{verbatim}
396    where the ``2'' can be replaced with a number that corresponds to the
397    number of CPUs available.
398    
399  Now you are ready to run the model. General instructions for doing so are  Now you are ready to run the model. General instructions for doing so are
400  given in section \ref{sect:runModel}. Here, we can run the model with:  given in section \ref{sect:runModel}. Here, we can run the model by
401    first creating links to all the input files:
402    \begin{verbatim}
403    ln -s ../input/* .
404    \end{verbatim}
405    and then calling the executable with:
406  \begin{verbatim}  \begin{verbatim}
407  ./mitgcmuv > output.txt  ./mitgcmuv > output.txt
408  \end{verbatim}  \end{verbatim}
409  where we are re-directing the stream of text output to the file {\em  where we are re-directing the stream of text output to the file
410  output.txt}.  \texttt{output.txt}.
   
411    
412  \subsection{Building/compiling the code elsewhere}  \subsection{Building/compiling the code elsewhere}
413    
# Line 948  the GNU g77 compiler and the mpich MPI l Line 796  the GNU g77 compiler and the mpich MPI l
796         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv         -machinefile mf --gm-kill 5 -v -np 2  ../build/mitgcmuv
797  \end{verbatim} }  \end{verbatim} }
798    
   
   
799  \section[Running MITgcm]{Running the model in prognostic mode}  \section[Running MITgcm]{Running the model in prognostic mode}
800  \label{sect:runModel}  \label{sect:runModel}
801    \begin{rawhtml}
802    <!-- CMIREDIR:runModel: -->
803    \end{rawhtml}
804    
805  If compilation finished succesfuully (section \ref{sect:buildingCode})  If compilation finished succesfully (section \ref{sect:buildingCode})
806  then an executable called \texttt{mitgcmuv} will now exist in the  then an executable called \texttt{mitgcmuv} will now exist in the
807  local directory.  local directory.
808    
809  To run the model as a single process (ie. not in parallel) simply  To run the model as a single process (\textit{ie.} not in parallel)
810  type:  simply type:
811  \begin{verbatim}  \begin{verbatim}
812  % ./mitgcmuv  % ./mitgcmuv
813  \end{verbatim}  \end{verbatim}
# Line 968  do!). The above command will spew out ma Line 817  do!). The above command will spew out ma
817  your screen.  This output contains details such as parameter values as  your screen.  This output contains details such as parameter values as
818  well as diagnostics such as mean Kinetic energy, largest CFL number,  well as diagnostics such as mean Kinetic energy, largest CFL number,
819  etc. It is worth keeping this text output with the binary output so we  etc. It is worth keeping this text output with the binary output so we
820  normally re-direct the {\em stdout} stream as follows:  normally re-direct the \texttt{stdout} stream as follows:
821  \begin{verbatim}  \begin{verbatim}
822  % ./mitgcmuv > output.txt  % ./mitgcmuv > output.txt
823  \end{verbatim}  \end{verbatim}
824    In the event that the model encounters an error and stops, it is very
825  For the example experiments in {\em verification}, an example of the  helpful to include the last few line of this \texttt{output.txt} file
826  output is kept in {\em results/output.txt} for comparison. You can compare  along with the (\texttt{stderr}) error message within any bug reports.
827  your {\em output.txt} with this one to check that the set-up works.  
828    For the example experiments in \texttt{verification}, an example of the
829    output is kept in \texttt{results/output.txt} for comparison. You can
830    compare your \texttt{output.txt} with the corresponding one for that
831    experiment to check that the set-up works.
832    
833    
834    
835  \subsection{Output files}  \subsection{Output files}
836    
837  The model produces various output files. At a minimum, the instantaneous  The model produces various output files and, when using \texttt{mnc},
838  ``state'' of the model is written out, which is made of the following files:  sometimes even directories.  Depending upon the I/O package(s)
839    selected at compile time (either \texttt{mdsio} or \texttt{mnc} or
840    both as determined by \texttt{code/packages.conf}) and the run-time
841    flags set (in \texttt{input/data.pkg}), the following output may
842    appear.
843    
844    
845    \subsubsection{MDSIO output files}
846    
847    The ``traditional'' output files are generated by the \texttt{mdsio}
848    package.  At a minimum, the instantaneous ``state'' of the model is
849    written out, which is made of the following files:
850    
851  \begin{itemize}  \begin{itemize}
852  \item \textit{U.00000nIter} - zonal component of velocity field (m/s and $>  \item \texttt{U.00000nIter} - zonal component of velocity field (m/s
853  0 $ eastward).    and positive eastward).
854    
855  \item \textit{V.00000nIter} - meridional component of velocity field (m/s  \item \texttt{V.00000nIter} - meridional component of velocity field
856  and $> 0$ northward).    (m/s and positive northward).
857    
858  \item \textit{W.00000nIter} - vertical component of velocity field (ocean:  \item \texttt{W.00000nIter} - vertical component of velocity field
859  m/s and $> 0$ upward, atmosphere: Pa/s and $> 0$ towards increasing pressure    (ocean: m/s and positive upward, atmosphere: Pa/s and positive
860  i.e. downward).    towards increasing pressure i.e. downward).
861    
862  \item \textit{T.00000nIter} - potential temperature (ocean: $^{0}$C,  \item \texttt{T.00000nIter} - potential temperature (ocean:
863  atmosphere: $^{0}$K).    $^{\circ}\mathrm{C}$, atmosphere: $^{\circ}\mathrm{K}$).
864    
865  \item \textit{S.00000nIter} - ocean: salinity (psu), atmosphere: water vapor  \item \texttt{S.00000nIter} - ocean: salinity (psu), atmosphere: water
866  (g/kg).    vapor (g/kg).
867    
868  \item \textit{Eta.00000nIter} - ocean: surface elevation (m), atmosphere:  \item \texttt{Eta.00000nIter} - ocean: surface elevation (m),
869  surface pressure anomaly (Pa).    atmosphere: surface pressure anomaly (Pa).
870  \end{itemize}  \end{itemize}
871    
872  The chain \textit{00000nIter} consists of ten figures that specify the  The chain \texttt{00000nIter} consists of ten figures that specify the
873  iteration number at which the output is written out. For example, \textit{%  iteration number at which the output is written out. For example,
874  U.0000000300} is the zonal velocity at iteration 300.  \texttt{U.0000000300} is the zonal velocity at iteration 300.
875    
876  In addition, a ``pickup'' or ``checkpoint'' file called:  In addition, a ``pickup'' or ``checkpoint'' file called:
877    
878  \begin{itemize}  \begin{itemize}
879  \item \textit{pickup.00000nIter}  \item \texttt{pickup.00000nIter}
880  \end{itemize}  \end{itemize}
881    
882  is written out. This file represents the state of the model in a condensed  is written out. This file represents the state of the model in a condensed
# Line 1020  form and is used for restarting the inte Line 884  form and is used for restarting the inte
884  there is an additional ``pickup'' file:  there is an additional ``pickup'' file:
885    
886  \begin{itemize}  \begin{itemize}
887  \item \textit{pickup\_cd.00000nIter}  \item \texttt{pickup\_cd.00000nIter}
888  \end{itemize}  \end{itemize}
889    
890  containing the D-grid velocity data and that has to be written out as well  containing the D-grid velocity data and that has to be written out as well
891  in order to restart the integration. Rolling checkpoint files are the same  in order to restart the integration. Rolling checkpoint files are the same
892  as the pickup files but are named differently. Their name contain the chain  as the pickup files but are named differently. Their name contain the chain
893  \textit{ckptA} or \textit{ckptB} instead of \textit{00000nIter}. They can be  \texttt{ckptA} or \texttt{ckptB} instead of \texttt{00000nIter}. They can be
894  used to restart the model but are overwritten every other time they are  used to restart the model but are overwritten every other time they are
895  output to save disk space during long integrations.  output to save disk space during long integrations.
896    
897    
898    
899    \subsubsection{MNC output files}
900    
901    Unlike the \texttt{mdsio} output, the \texttt{mnc}--generated output
902    is usually (though not necessarily) placed within a subdirectory with
903    a name such as \texttt{mnc\_test\_\${DATE}\_\${SEQ}}.  The files
904    within this subdirectory are all in the ``self-describing'' netCDF
905    format and can thus be browsed and/or plotted using tools such as:
906    \begin{itemize}
907    \item \texttt{ncdump} is a utility which is typically included
908      with every netCDF install:
909      \begin{rawhtml} <A href="http://www.unidata.ucar.edu/packages/netcdf/"> \end{rawhtml}
910    \begin{verbatim}
911    http://www.unidata.ucar.edu/packages/netcdf/
912    \end{verbatim}
913      \begin{rawhtml} </A> \end{rawhtml} and it converts the netCDF
914      binaries into formatted ASCII text files.
915    
916    \item \texttt{ncview} utility is a very convenient and quick way
917      to plot netCDF data and it runs on most OSes:
918      \begin{rawhtml} <A href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html"> \end{rawhtml}
919    \begin{verbatim}
920    http://meteora.ucsd.edu/~pierce/ncview_home_page.html
921    \end{verbatim}
922      \begin{rawhtml} </A> \end{rawhtml}
923      
924    \item MatLAB(c) and other common post-processing environments provide
925      various netCDF interfaces including:
926      \begin{rawhtml} <A href="http://mexcdf.sourceforge.net/"> \end{rawhtml}
927    \begin{verbatim}
928    http://mexcdf.sourceforge.net/
929    \end{verbatim}
930      \begin{rawhtml} </A> \end{rawhtml}
931      \begin{rawhtml} <A href="http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html"> \end{rawhtml}
932    \begin{verbatim}
933    http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html
934    \end{verbatim}
935      \begin{rawhtml} </A> \end{rawhtml}
936    \end{itemize}
937    
938    
939  \subsection{Looking at the output}  \subsection{Looking at the output}
940    
941  All the model data are written according to a ``meta/data'' file format.  The ``traditional'' or mdsio model data are written according to a
942  Each variable is associated with two files with suffix names \textit{.data}  ``meta/data'' file format.  Each variable is associated with two files
943  and \textit{.meta}. The \textit{.data} file contains the data written in  with suffix names \texttt{.data} and \texttt{.meta}. The
944  binary form (big\_endian by default). The \textit{.meta} file is a  \texttt{.data} file contains the data written in binary form
945  ``header'' file that contains information about the size and the structure  (big\_endian by default). The \texttt{.meta} file is a ``header'' file
946  of the \textit{.data} file. This way of organizing the output is  that contains information about the size and the structure of the
947  particularly useful when running multi-processors calculations. The base  \texttt{.data} file. This way of organizing the output is particularly
948  version of the model includes a few matlab utilities to read output files  useful when running multi-processors calculations. The base version of
949  written in this format. The matlab scripts are located in the directory  the model includes a few matlab utilities to read output files written
950  \textit{utils/matlab} under the root tree. The script \textit{rdmds.m} reads  in this format. The matlab scripts are located in the directory
951  the data. Look at the comments inside the script to see how to use it.  \texttt{utils/matlab} under the root tree. The script \texttt{rdmds.m}
952    reads the data. Look at the comments inside the script to see how to
953    use it.
954    
955  Some examples of reading and visualizing some output in {\em Matlab}:  Some examples of reading and visualizing some output in {\em Matlab}:
956  \begin{verbatim}  \begin{verbatim}
# Line 1059  Some examples of reading and visualizing Line 967  Some examples of reading and visualizing
967  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end  >> for n=1:11; imagesc(eta(:,:,n)');axis ij;colorbar;pause(.5);end
968  \end{verbatim}  \end{verbatim}
969    
970    Similar scripts for netCDF output (\texttt{rdmnc.m}) are available and
971    they are described in Section \ref{sec:pkg:mnc}.
972    
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